Determination of pair-wise inter-residue interaction forces from folding pathways and their implementation in coarse-grained folding prediction

Phys Chem Chem Phys. 2009 Mar 28;11(12):1949-61. doi: 10.1039/b820801h. Epub 2009 Feb 20.

Abstract

Interaction forces among residue pairs are determined from optimum folding pathways along which a protein represented as a coarse-grained chain of alpha-carbons goes from different initial configurations to a known native state. A dynamic optimization approach is employed that uses the coarse-grained model to compute the optimal folding pathways. The pair-wise interaction forces obtained in this manner are incorporated into the coarse-grained model which is then simulated to fold the protein from a new set of initial configurations in a predictive way. We show that the folding pathways predicted in this manner are near-optimal. We applied the technique to the secondary structures: helix and beta-sheet.

MeSH terms

  • Computer Simulation*
  • Models, Chemical*
  • Protein Folding*
  • Protein Structure, Secondary
  • Thermodynamics*